Strange power hiccup on m2-atx when turning my car off.

I recently changed my car PC installation over to another motherboard and as a result changed my power supply back to the m2-atx. Keeping all the components (Power, USB etc) the same i figured it'd be an easy deal. I am now having a problem that i really dont know where to begin troubleshooting. Basically the power to my car PC dips down to <9volts whenever i take my key out of the ignition. It only happens for a second before the multimeter jumps back up to 12v, but its long enough that the m2 cant compensate for the dip and keep my system alive. I can hear the processor fan speed slow for a second before it picks back up and the computer reboots.

The thing thats kinda baffling me is this really shouldn't be happening. Both of my batteries are less than a year old and the auxiliary battery powers nothing but the car PC and a single (but new) amplifier. I never run the system with the engine off and both batteries still test fine. So where should i start checking? Could a loose wire cause the problem? Again, i'm using all the same wiring, same battery isolator etc. What could cause a dip in detected voltage from a healthy battery?